H5S: HDF5 Dataspace Interface
In patperry/rhdf5: HDF5 interface to R

Description Usage Arguments Details Value Author(s) References See Also Examples

These functions create and manipulate the dataspace in which to store the elements of a dataset.

H5Screate                 (type = h5default("H5S"))
H5Screate_simple          (dims, maxdims = dims)
H5Scopy                   (h5space)
H5Sclose                  (h5space)
H5Sis_simple              (h5space)
H5Sget_simple_extent_dims (h5space)
H5Sselect_hyperslab       (h5space, op = h5default("H5S_SELECT"), 
			     start = NULL, stride = NULL, count = NULL, block = NULL)
H5Sselect_index           (h5space, index)

`type`	See `h5const("H5S")` for possible types.
`dims`	Dimension of the dataspace. This argument is similar to the dim attribute of an array. When viewing the HDF5 dataset with an C-program (e.g. HDFView), the dimensions appear in inverted order, because the fastest changing dimension in R is the first one, and in C its the last one.
`maxdims`	Maximum extension of the dimension of the dataset in the file.
`h5space`	An object of class `H5IdComponent` representing a H5 dataspace identifier. See `H5Dget_space`, `H5Screate_simple`, `H5Screate` to create an object of this kind.
`index`	A list of integer indices. The length of the list corresponds to the number of dimensions of the HDF5 array.
`op`	See h5const("H5S_SELECT") for possible arguments.
`start`	The start coordinate of a hyperslab (similar to subsetting in R). Counting is R-style 1-based.
`stride`	The stride of the hypercube. Read the introduction http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html before using this argument. R behaves like Fortran in this example.
`count`	The number of blocks to be written.
`block`	The block size of the hyperslab. Read the introduction http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html before using this argument. R behaves like Fortran in this example.

Interface to the HDF5 C-library libhdf5. See http://www.hdfgroup.org/HDF5/doc/RM/RM_H5S.html for further details.

As an introduction to use hyperslabs see these tutorials: See these introductions to hyperslabs: http://www.hdfgroup.org/HDF5/Tutor/selectsimple.html, http://www.hdfgroup.org/HDF5/Tutor/select.html and http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html. Please note that in R the first dimension is the fastest changing dimension. When viewing the HDF5 datasets with any C-program (e.g. HDFView), the order of dimensions is inverted. In the R interface counting starts with 1, whereas in the C-programs (e.g. HDFView) counting starts with 0.

H5Sselect_index is not part of the standard HDF5 C interface. It performes an iterative call to H5select_points by iterating through the given index positions. This function avoids a for loop in R. If a list element is NULL, all elements of the respective dimension are considered.

H5Screate, H5Screate_simple, and H5Scopy return an object of class H5IdComponent representing a dataspace.

H5Sis_simple returns a boolean.

H5Sget_simple_extent_dims returns an integer vector.

The other functions return the standard return value from their respective C-functions.

Bernd Fischer

http://www.hdfgroup.org/HDF5

rhdf5

sid <- H5Screate_simple(c(10,5,3))
sid
H5Sis_simple(sid)
H5Sget_simple_extent_dims(sid)

# select a subarray (called hyperslab in the hdf5 community).
# The next h5write can use this to write a subarray
H5Sselect_index(sid, list(1:3,2:4,2))

# always close dataspaces after usage to free recources
H5Sclose(sid)
sid